CampyGStyper

Campylobacter Gnomic Species Typer. A python script for accurate assignment of ANI genomic species to Campylobacter genomes.

Installation

with conda/mamba - NOT YET AVAILABLE

conda install -c bioconda campygstyper

without conda

git clone https://github.com/LanLab/campygstyper.git

cd campygstyper

python setup.py install

Note following dependencies must be installed

• fastANI

Usage

campygstyper [-h] -i QUERYFOLDER -o OUTPUTFILE [-t THREADS]

-h, --help show this help message and exit

-i,--query QUERY folder containing all input genomes (genomes must have *.fasta suffix)

-o,--output tabular output file with classifications for each genome in query folder

-t, --thread number of threads to run fastANI with (default: 4)

Outputs

A tab delimited file with the following columns:

• Query Genome : genome name extracted from file name
• Highest ANI Value : The highest ANI value of the query when compared to all centroid genomes
• Matching centroid genome : The accession of the highest matching centroid genome
• ANI cluster number : The cluster number that the centroid genome represents
• Campylobacter Genomic Species : The genomic species name assigned to the matching ANI cluster
• Possible Novel genomic species : Whether or not this genome does not match any centroid genome at 94.2% ANI. If True no centroid genomes match indicating that the genome could represent a new species. If True, highest match for other columns is still included but is not reliable.